Genomics 4-6 Flashcards by Liam Tasker

What is the central dogma who designed it ?

DNA>RNA>Protein

Francis crick

How well did you know this?

Not at all

Perfectly

What are the 4 model bacteria ?

Eschericha coli -
Neisseria meningitidis -
Heliobacter pylori -
Bacillus subtilis +

How well did you know this?

Not at all

Perfectly

Name the 6 strains of E.coli

EPEC- Enteropathogenic e.coli
EHEC- Enterohaemorrhagic e.coli 
ETEC- Enterotoxigenic e.coli
EAEC- Enteroaggregative e.coli
EIEC- Enteroinvasive e.coli
DAEC- Diffusely adherent e.coli

How well did you know this?

Not at all

Perfectly

What is a pathogencity island ?

a series of contiguous genes including one or more that determines virulence, acquired by horizontal gene transfer. It is transposable.

How well did you know this?

Not at all

Perfectly

What type of E.coli attacks the colon and secretes Shigatoxin ?

EHEC- Enterohaemorrhagic e.coli

How well did you know this?

Not at all

Perfectly

What type of E.coli is taken up by cytosis and forms an actin tale ?

EIEC- Enteroinvasive e.coli

How well did you know this?

Not at all

Perfectly

What is unique about DAEC- Diffusely adherent e.coli ?

Uses villi for protection

How well did you know this?

Not at all

Perfectly

What does EAEC- Enteroaggregative e.coli form ?

Biofilm

How well did you know this?

Not at all

Perfectly

What E.coli secretes a temperature sensitive toxin ?

Enterotoxigenic e.coli- Stable and labile enterotoxins

How well did you know this?

Not at all

Perfectly

What does enteropathogenic e.coli do to the villi ?

Changes physiological structure and secretes type 3 effective molecules into the cell that take over actin cytoskeleton.

How well did you know this?

Not at all

Perfectly

What is natural competence ?

The ability to take up DNA from the environment

How well did you know this?

Not at all

Perfectly

What model bacteria use the pseudo type IV pilus system ?

Bacillus subtilis

Neisseria meningitidis

How well did you know this?

Not at all

Perfectly

What allows heliobacter pylori to be naturally competent ?

Type IV secretion system

How well did you know this?

Not at all

Perfectly

What do optical tweezers measure in terms of DNA uptake ?

Measures the force that DNA is being pulled into the cell

How well did you know this?

Not at all

Perfectly

What allows nerisseria meningitidis to take up DNA that is specific to nerisseria genus ?

Uses a minor pilin (ComP) combined with a major pilin (PiLE)

How well did you know this?

Not at all

Perfectly

What do all of the DNA uptake systems have in common ?

All require ATP dependent stripping of the dsDNA to ssDNA.

How well did you know this?

Not at all

Perfectly

What is the pathogenecity island in heliobacter pylori ?

Cag- Continually takes up DNA and alters genome.

How well did you know this?

Not at all

Perfectly

What allows DNA to pass through the outer membrane of neisseria meningitidis ?

A secreton

What is the pilus made up of in bacillus subtilis and what are the bonds holding the proteins together ?

ComGC protein and disulphide bonds

What are the minimum standards provided by genomic consortium ?

A table dedicated to classification.
A table dedicated to project info.
A table dedicated to genome statistics
A table dedicated to COG database

What is special about the genome of borrellia burgdoferi ?

Contains linear chromosomes and linear and circular plasmids.

What is a replicon ?

A region of DNA that replicates from a single origin of replication.

What limits 16s rRNA sequences from being a good determining factor for phylogentic relationships ?

There tends to be more than 1 copy of genes

16s rRNA sequences can vary alot even within the same genome

What is a biosynthetic cluster ?

A physical cluster of of 2 or more genes in a genome that together encode for a pathway which produces a metabolite

What do CRISPR molecules do ?

Play a role in bacteria defence against phage attack | Allows uptake of exogenous genetic material

What are the families of bioactive secondary metabolites ?

PKs NRPs RiPPs isoprenoids

What is the benefit of whole genome sequencing ?

Allows whole genome comp

What is the problem with identifying genomes by similarity ?

A third of genes have insufficient similarity | Similarity based on function is often wrong

How can microarrays be used for the identification of gene function ?

By knocking out the gene being identified for function and growing the bacteria in different growth conditions and then comparing to reference strain

What is a cryptic prophage ?

A phage that integrates in the genome but have lost function.

Why are cryptic phages retained ?

Essential for growth under stressful conditions

What are the limitations of random barcode transposon site sequencing ?

Cannot recreate natural environment Knock out gene may not show in phenotype due to synthetic lethality (other proteins producing the knock out gene product)

What has random barcode transposon site sequencing allowed for ?

Allows genes of unknown function to be given a putative function as it allows comparison of multiple genomes at once Higher throughput than microarrays

What has transposon directed insertion site sequencing allowed for ?

Allows core genes for infection and colonisation to be found as bacteria are injected into real life environments

During random barcode transposon site sequencing what allows for the identification of the unique knockouts ?

PCR using primers that are specific to the adapters that have been added and the barcoded transposon.

During random barcode transposon site sequencing what allows for multiple species to be studied at once ?

A second primer added into the PCR

What sort of dye do microarrays contain ?

Tetrazolium

What does random barcode transposon site sequencing do ?

Creates library of knock outs all over the genome with an associated barcode to each unique knock out.

What are the limitations of phenotypic microarray analysis ?

Low through put as a compromise of high number of mutants or high number of environmental conditions has to be made

In B. subtilis, what does the inactivation of comEC (large polytopic transmembrane protein) prevent ?

prevents not only uptake of DNA, but also the degradation of the nontransforming strand

In Bacillus subtilis what does ComFA do and what does it contain to allow this ?

Helicase and translocase motifs | Allows stripping of dsDNA and movement of ssDNA

What do the binding proteins in Bacillus subtilis allow and do ?

Cover the DNA allowing it to be replicated and transferred into the chromosome

What is the only DNA sequence Neisseria meningitidis recognises ?

GCCGTCTGAA | Known as DNA uptake sequence

What is the major protein on heliobacter pylori's uptake system ?

ComB9